DOCSLIB.ORG

Cops2 Promotes Pluripotency Maintenance by Stabilizing Nanog Protein and Repressing Transcription

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Cops2 Promotes Pluripotency Maintenance by Stabilizing Nanog Protein and Repressing Transcription www.nature.com/scientificreports OPEN Cops2 promotes pluripotency maintenance by Stabilizing Nanog Protein and Repressing Received: 30 March 2016 Accepted: 10 May 2016 Transcription Published: 26 May 2016 Weiyu Zhang1,*, Peiling Ni1,*, Chunlin Mou1,*, Yanqin Zhang1,*, Hongchao Guo1,2,*, Tong Zhao1, Yuin-Han Loh2,3 & Lingyi Chen1,4 The COP9 signalosome has been implicated in pluripotency maintenance of human embryonic stem cells. Yet, the mechanism for the COP9 signalosome to regulate pluripotency remains elusive. Through knocking down individual COP9 subunits, we demonstrate that Cops2, but not the whole COP9 signalosome, is essential for pluripotency maintenance in mouse embryonic stem cells. Down- regulation of Cops2 leads to reduced expression of pluripotency genes, slower proliferation rate, G2/M cell cycle arrest, and compromised embryoid differentiation of embryonic stem cells. Cops2 also facilitates somatic cell reprogramming. We further show that Cops2 binds to Nanog protein and prevent the degradation of Nanog by proteasome. Moreover, Cops2 functions as transcriptional corepressor to facilitate pluripotency maintenance. Altogether, our data reveal the essential role and novel mechanisms of Cops2 in pluripotency maintenance. Embryonic stem cells (ESCs) are able to self-renew indefinitely, and have the potential to differentiate into all types of cells in the adult organism. The unique property of ESCs, namely pluripotency, renders ESCs as a prom- ising cell source in regenerative medicine and cell replacement therapy. Transcriptional regulation plays a critical role in pluripotency maintenance of ESCs1,2. Previous studies found that three transcription factors Oct4, Nanog and Sox2 regulate each other and form a core transcriptional regulatory circuitry underlying pluripotency main- tenance3. This core regulatory circuitry not only activates the expression of pluripotency-associated genes, but also suppresses the expression of differentiation-related genes3. Meanwhile, many other pluripotency associated transcription factors and coactivators, including Klf4, Sall4, Esrrb and Ncoa3, regulate the three genes of the core regulatory circuitry, forming an expanded pluripotency regulatory network and allowing signaling pathways integrated into transcriptional regulation4–8. In addition, the core components of the pluripotency network are regulated at protein level through post-translational modifications. For example, phosphorylation of Ser/Thr-Pro motifs of Nanog promotes the interaction between Nanog and Pin1, and stabilizes Nanog protein9. Both Oct4 and Sox2 are modified with O-linked-N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation of Thr 228 enhances the transcriptional activity of Oct4, and regulates the functions of Oct4 in maintaining ESC self-renewal and reprogramming somatic cells10. The COP9 signalosome (CSN), composed of 8 subunits (Cops1 to Cops8), is highly conserved from yeast to human11–13. The most studied CSN function is to regulate protein degradation. The CSN suppresses the activity of the cullin-RING-E3 ligases (CRL) through deneddylation of cullins, thus enhancing protein stability14,15. It also regulates the ubiquitin ligase COP1, consequently the degradation of COP1 substrates16. Moreover, CSN-associated deubiquitinating enzymes, Ubp12 in yeast and USP15 in mammals, may stabilize the adaptor subunits of CRL and 1State Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center for Biotherapy, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Protein Sciences and College of Life Sciences, Nankai University, Tianjin 300071, China. 2Epigenetics and Cell Fates Laboratory, A* STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore. 3Department of Biological Sciences, National University of Singapore, Singapore. 4State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Chinese Academy of Medical Sciences, Beijing 100021, China. *These authors contributed equally to this work. Correspondence and requests for materials should be addressed to Y.-H.L. (email: yhloh@ imcb.a-star.edu.sg) or L.C. (email: [email protected]) SCIENTIFIC REPORTS | 6:26804 | DOI: 10.1038/srep26804 1 www.nature.com/scientificreports/ Iκ Bα , respectively, through deubiquitination17,18. In addition to regulation of protein degradation, the CSN is also involved in transcriptional regulation, protein phosphorylation and subcellular distribution19–23. While the CSN functions as a complex, CSN subunits may also have their own functions independent of the CSN complex. For example, Alien, a variant of Cops2, has been demonstrated to be a transcriptional corepressor24,25. Through a whole-genome RNAi screening experiment, it has been shown that down-regulation of CSN subu- nits, COPS1, COPS2 and COPS4, reduces the expression of the OCT4-GFP reporter in human ESCs, indicating a role of the CSN in pluripotency maintenance26. Consistent with this observation, some CSN subunits are required for mouse embryo development. Homozygous knockout of Cops2, Cops3, Cops5, Cops6, or Cops8 in mice, leads to early embryo death27–31. No ESCs could be derived from Cops2 or Cops8 null blastocysts, implying that the CSN is involved in pluripotency establishment29,30. Yet, Cops2, Cops3, Cops5, Cops6, or Cops8 knockout embryos die at different embryonic days ranging from day 6.5 to 8.5, implying that individual CSN subunits have their own biological functions, in addition to the function of the CSN. It is not clear whether the whole CSN complex or individual CSN subunits are required for pluripotency maintenance, and how the CSN or individual CSN subu- nits contribute to pluripotency maintenance. To elucidate the function and mechanisms of the CSN in pluripotency maintenance, we knocked down individual CSN subunits in mouse ESCs, and found that only Cops2 is essential for pluripotency maintenance in mouse ESCs. We further demonstrated that Cops2 stabilizes Nanog protein through direct interaction. In addition, Cops2 func- tions as a transcriptional corepressor to suppress gene expression, including 2-cell-stage embryo specific (2C) genes. In summary, our data revealed that Cops2, but not the CSN, is required for pluripotency maintenance in mouse ESCs. Results To clarify the role of CSN subunits in pluripotency maintenance, we examined the expression of pluripotency genes, Nanog, Oct4, and Sox2, upon knocking down each CSN subunit by shRNA in mouse ESCs (Fig. 1a). In con- trast to the RNAi screening data in human ESCs26, only knockdown (KD) of Cosp2, but not any other CSN sub- units, reduces the expression of Nanog and Oct4 mRNA (Fig. 1b). To rule out the possibility of shRNA off-target effect, the regulatory effect of Cops2 on Nanog and Oct4 at both RNA and protein levels was further validated with another shRNA targeting Cops2 (Fig. 1c,d). In addition, differentiation markers of three germ layers and the trophectoderm (TE), except for the ectodermal marker Pax6, are up-regulated upon Cops2 KD in ESCs (Fig. 1e), implicating compromised pluripotent status in Cops2 KD ESCs. To further characterize the role of Cops2 in ESCs, we attempted to establish stable Cops2 KD ESCs. ESCs were transfected with plasmids expressing shRNAs targeting GFP and CSN subunits. Much less Cops2 KD colonies (less than 10 colonies per experiment) grew up after 7–10 day puromycin selection, compared to other CSN subunits and GFP KD ESCs (ranging from 50 to 280 colonies) (Supplementary Table S1). Moreover, Cops2 is inefficiently knocked down in the survivingCops2 KD ESC clones (Supplementary Fig. S1). These data imply that Cops2 is essential for the self-renewal of ESCs. We then switched to knock down Cops2 transiently in ESCs. KD of Cops2 impairs the alkaline phosphatase (AP) positivity in ESCs, while Cops8 KD does not affect the expression of AP (Fig. 2a). In addition, Cops2 KD slows down the proliferation of ESCs, likely due to G2/M arrest, but not cell apoptosis (Fig. 2b–d). Consistent with the slower proliferation rate of Cops2 KD ESCs, the colony forming ability of ESCs is also reduced upon Cops2 KD (Fig. 2e). All these data indicate that KD of Cops2 compromises the self-renewal of ESCs. Next, we sought to characterize whether Cops2 KD affects the differentiation potential of ESCs. Embryoid bodies (EBs) formed by Cops2 KD ESCs are smaller than control GFP KD EBs (Fig. 2f). Moreover, most of the differentiation markers are not fully activated in Cops2 KD EBs, particularly the ectodermal markers Nestin and Pax6 (Fig. 2g), implying that the differentiation potential of ESCs is impaired upon Cops2 KD. To address whether Cops2 plays a role in somatic cell reprogramming, Cops2 was knocked down or over- expressed in mouse embryonic fibroblasts (MEFs), which were co-infected with retroviruses expressing Oct4, Sox2, Klf4 and c-Myc. Cops2 KD reduces the reprogramming efficiency, while overexpression ofCops2 increases the number of AP positive colonies after reprogramming (Fig. 2h,i), implicating that Cops2 facilitates Yamanaka factors to reprogram somatic cells. It is noticeable that the down-regulation of Nanog is more eminent at protein level than at RNA level (Fig. 1c,d), implying that Cops2 might regulate Nanog protein stability. To understand how Cops2 regulates the expression of Nanog, through transcriptional regulation or by affecting Nanog protein stability, we first performed luciferase reporter assay using a 6-kb Nanog promoter. KD of Cops2 does not affect
Load more

Recommended publications
  • Analysis of Trans Esnps Infers Regulatory Network Architecture
    Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation.
    [Show full text]
  • Seq2pathway Vignette
    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
    [Show full text]
  • Cops5 Safeguards Genomic Stability of Embryonic Stem Cells Through Regulating Cellular Metabolism and DNA Repair
    Cops5 safeguards genomic stability of embryonic stem cells through regulating cellular metabolism and DNA repair Peng Lia, Lulu Gaoa, Tongxi Cuia, Weiyu Zhanga, Zixin Zhaoa, and Lingyi Chena,1 aState Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Collaborative Innovation Center for Biotherapy, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, 300071 Tianjin, China Edited by Janet Rossant, Hospital for Sick Children, University of Toronto, Toronto, Canada, and approved December 24, 2019 (received for review August 29, 2019) The highly conserved COP9 signalosome (CSN), composed of 8 transiently expressed in about 5% of ESCs at a given time, subunits (Cops1 to Cops8), has been implicated in pluripotency promotes rapid telomere elongation by telomere recombination maintenance of human embryonic stem cells (ESCs). Yet, the mech- and regulates genomic stability (11). Induced by genotoxic stress, anism for the CSN to regulate pluripotency remains elusive. We Filia stimulates the PARP1 activity and relocates from centro- previously showed that Cops2, independent of the CSN, is essential somes to DNA damage sites and mitochondria to regulate DDR for the pluripotency maintenance of mouse ESCs. In this study, we and apoptosis (12). Sall4, a pluripotency transcription factor, set out to investigate how Cops5 and Cops8 regulate ESC differ- facilitates the ataxia telangiectasia-mutated activation in re- entiation and tried to establish Cops5 and Cops8 knockout (KO) sponse to DSBs (13). To minimize the ROS-induced genomic ESC lines by CRISPR/Cas9. To our surprise, no Cops5 KO ESC clones DNA damage, ESCs produce lower levels of mitochondrial ROS were identified out of 127 clones, while three Cops8 KO ESC lines and express higher levels of antioxidants than differentiated cells were established out of 70 clones.
    [Show full text]
  • Sex Determination: a 'Window' of DAX1 Activity
    Review TRENDS in Endocrinology and Metabolism Vol.15 No.3 April 2004 Sex determination: a ‘window’ of DAX1 activity Louisa M. Ludbrook and Vincent R. Harley Prince Henry’s Institute of Medical Research, PO Box 5152, Clayton, VIC 3168, Australia Traditionally, DAX1 was considered an ‘anti-testis’ gene that are probably important for male sex determination because DAX1 duplications in XY individuals cause have yet to be identified, because some 75% of sex reversal male-to-female sex reversal: dosage-sensitive sex rever- cases remain unexplained genetically [15]. Some progress sal (DSS). In DSS, two active DAX1 genes on one has been made in deciphering the roles and complex X chromosome can abrogate testis formation. By con- relationships of the known sex-determining genes during trast, mutations and deletions of DAX1 cause adrenal gonadogenesis. Here, we describe the emerging role of hypoplasia congenita (AHC). Although AHC patients DAX1 in male testis formation and discuss the possible develop testes, gonadal defects include disorganized molecular mechanisms through which DAX1 regulates testis cords and hypogonadotropic hypogonadism, this pathway. which is not completely restored with gonadotropin or androgen therapy. Recent evidence of XY sex reversal Expression of DAX1 in Dax1-deficient mice strongly supports a role for Dax1 DAX1 RNA expression is restricted to certain tissue types as a ‘pro-testis’ gene. Therefore, perhaps DAX1/Dax1 and is largely coexpressed with SF1, also crucial for both acts within a ‘window’ of activity, outside of which tes- adrenal and gonadal development [16–18]. Based on in tis formation does not occur. Here, we discuss the func- situ hybridization analyses, Sf1 and Dax1 are expressed in tion and possible mechanisms of DAX1 action in male both developing and adult adrenal, gonadal, hypothalamic gonadogenesis.
    [Show full text]
  • Characterization of Transcription Factor Complexes Involved in Globin Gene Regulation
    Characterization of Transcription Factor Complexes involved in Globin Gene Regulation Katarzyna Ewa Kołodziej 26th March 2008 Cover: Rodota The work presented in this thesis was performed at the Department of Cell Biology at the Erasmus Univer- sity Medical Center Rotterdam. This department is member of the Medisch Genetisch Centrum Zuid-West Nederland. The research was partially supported by the Netherlandse Organizatie voor Wetenschappelijk Onderzoek (NWO) and by EU. Characterization of Transcription Factor Complexes involved in Globin Gene Regulation Karakterizering van transcriptie factor complexen betrokken bij de regulatie van globine genen PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Erasmus Universiteit Rotterdam op gezag van de Rector Magnificus Prof.dr. S.W.J. Lamberts en volgens besluit van het College voor Promoties. De openbare verdediging zal plaatsvinden op woensdag 26 maart 2008 om 15.45 uur. door Katarzyna Ewa Kołodziej geboren te Wrocław, Polen Promotiecommissie Promotor: Prof.dr. F.G. Grosveld Overige laden: Prof.dr. J.N.J. Philipsen Prof.dr. J.D. Engel Dr.ir. D.N. Meijer Copromotor: Dr. J. Strouboulis Moim rodzicom & for Luc TABLE OF CONTENTS Chapter 1 : Introduction 9 Chapter 2 : Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads (Patrick Rodriguez, Harald Braun, Katarzyna E. Kolodziej, Ernie de Boer, Jennifer Campbel, Edgar Bonte, Sjaak Philipsen and John Strouboulis Methods Mol Bio. 2006; 338: 305-23 ) 33 Chapter 3 : GATA-1 forms distinct activating and repressive complexes in erythroid cells (Patrick Rodriguez, Edgar Bonte, Jeroen Krijgsveld, Katarzyna E. Kolodziej, Boris Guyot, Albert Heck, Paresh Vyas, Ernie de Boer, Frank Grosveld and John Strouboulis, EMBO J.
    [Show full text]
  • Steroid Receptor Coactivator-1-Deficient Mice Exhibit Altered Hypothalamic-Pituitary-Adrenal Axis Function
    0013-7227/06/$15.00/0 Endocrinology 147(3):1322–1332 Printed in U.S.A. Copyright © 2006 by The Endocrine Society doi: 10.1210/en.2005-0751 Steroid Receptor Coactivator-1-Deficient Mice Exhibit Altered Hypothalamic-Pituitary-Adrenal Axis Function Jonathon N. Winnay, Jianming Xu, Bert W. O’Malley, and Gary D. Hammer Departments of Molecular and Integrative Physiology (H.N.W., G.D.H.) and Internal Medicine (G.D.H.), Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48109-0678; and Department of Molecular and Cellular Biology, Baylor College of Medicine (J.X., B.W.O.), Houston, Texas 77030 Downloaded from https://academic.oup.com/endo/article/147/3/1322/2501069 by guest on 28 September 2021 Steroidogenic factor-1 (SF-1), has emerged as a critical nu- as well as a concomitant defect in glucocorticoid-mediated clear receptor regulating development and differentiation at feedback inhibition of the HPA axis. An examination of po- several levels of the hypothalamic-pituitary-steroidogenic tential compensatory mechanism(s) revealed an increase in axis. Although many coregulatory factors have been shown to adrenal weight, selective elevation of melanocortin 2 receptor physically and functionally interact with SF-1, the relative mRNA, and a coincident increase in SRC-2 and SRC-3 expres- importance of these interactions in SF-1 target tissues has not sion in SRC-1؊/؊ adrenals. A reduction in blood glucose was been thoroughly established. In this study we assessed roles observed in SRC-1؊/؊ mice after chronic stress, consistent of steroid receptor coactivator-1 (SRC-1) in hypothalamic-pi- with a generalized state of glucocorticoid resistance.
    [Show full text]
  • Regulatory Mechanisms Underlying Sepsis Progression in Patients with Tumor Necrosis Factor‑Α Genetic Variations
    EXPERIMENTAL AND THERAPEUTIC MEDICINE 12: 323-328, 2016 Regulatory mechanisms underlying sepsis progression in patients with tumor necrosis factor‑α genetic variations * * YANGZHOU LIU , NING HAN , QINCHUAN LI and ZENGCHUN LI Emergency Trauma Department, Shanghai East Hospital, Shanghai 200120, P.R. China Received November 4, 2014; Accepted November 18, 2015 DOI: 10.3892/etm.2016.3308 Abstract. The present study aimed to investigate the regula- and ubiquitination of the FUS protein. Furthermore, COPS2 tory mechanisms underlying sepsis progression in patients with and CUL3 may be novel targets of miR-15. tumor necrosis factor (TNF)-α genetic variations. The GSE5760 expression profile data, which was downloaded from the Gene Introduction Expression Omnibus database, contained 30 wild-type (WT) and 28 mutation (MUT) samples. Differentially expressed Multiple trauma, which is commonly associated with severe inju- genes (DEGs) between the two types of samples were identified ries and multiple organ failure, may lead to various complications, using the Student's t-test, and the corresponding microRNAs including sepsis and septic shock, which are major healthcare (miRNAs) were screened using WebGestalt software. An problems worldwide (1-3). There are 400,000-500,000 cases of integrated miRNA-DEG network was constructed using the sepsis in the United States annually (4). Antimicrobial therapy Cytoscape software, based on the interactions between the may be applied for the management of sepsis; however, the DEGs, as identified using the Search Tool for the Retrieval mortality rate associated with sepsis has increased, and was of Interacting Genes/Proteins database, and the correlation reported to be as high as 40% in 2003 (5).
    [Show full text]
  • COPS2 Antibody Cat
    COPS2 Antibody Cat. No.: 28-027 COPS2 Antibody Antibody used in WB on Human, Mouse at 1:200. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Dog, Drosophila, Human, Mouse, Rat, Zebrafish Antibody produced in rabbits immunized with a synthetic peptide corresponding a region IMMUNOGEN: of human COPS2. TESTED APPLICATIONS: ELISA, WB COPS2 antibody can be used for detection of COPS2 by ELISA at 1:312500. COPS2 APPLICATIONS: antibody can be used for detection of COPS2 by western blot at 1.25 μg/mL, and HRP conjugated secondary antibody should be diluted 1:50,000 - 100,000. POSITIVE CONTROL: 1) Cat. No. XBL-10409 - Fetal Liver Tissue Lysate PREDICTED MOLECULAR 52 kDa WEIGHT: September 27, 2021 1 https://www.prosci-inc.com/cops2-antibody-28-027.html Properties PURIFICATION: Antibody is purified by protein A chromatography method. CLONALITY: Polyclonal CONJUGATE: Unconjugated PHYSICAL STATE: Liquid Purified antibody supplied in 1x PBS buffer with 0.09% (w/v) sodium azide and 2% BUFFER: sucrose. CONCENTRATION: batch dependent For short periods of storage (days) store at 4˚C. For longer periods of storage, store STORAGE CONDITIONS: COPS2 antibody at -20˚C. As with any antibody avoid repeat freeze-thaw cycles. Additional Info OFFICIAL SYMBOL: COPS2 ALTERNATE NAMES: COPS2, CSN2, SGN2, ALIEN, TRIP15 ACCESSION NO.: NP_004227 PROTEIN GI NO.: 4759264 GENE ID: 9318 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References COPS2 is an essential component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the BACKGROUND: deneddylation of the cullin subunits of SCF-type E3 ligase complexes.
    [Show full text]
  • Development of Novel Analysis and Data Integration Systems to Understand Human Gene Regulation
    Development of novel analysis and data integration systems to understand human gene regulation Dissertation zur Erlangung des Doktorgrades Dr. rer. nat. der Fakult¨atf¨urMathematik und Informatik der Georg-August-Universit¨atG¨ottingen im PhD Programme in Computer Science (PCS) der Georg-August University School of Science (GAUSS) vorgelegt von Raza-Ur Rahman aus Pakistan G¨ottingen,April 2018 Prof. Dr. Stefan Bonn, Zentrum f¨urMolekulare Neurobiologie (ZMNH), Betreuungsausschuss: Institut f¨urMedizinische Systembiologie, Hamburg Prof. Dr. Tim Beißbarth, Institut f¨urMedizinische Statistik, Universit¨atsmedizin, Georg-August Universit¨at,G¨ottingen Prof. Dr. Burkhard Morgenstern, Institut f¨urMikrobiologie und Genetik Abtl. Bioinformatik, Georg-August Universit¨at,G¨ottingen Pr¨ufungskommission: Prof. Dr. Stefan Bonn, Zentrum f¨urMolekulare Neurobiologie (ZMNH), Referent: Institut f¨urMedizinische Systembiologie, Hamburg Prof. Dr. Tim Beißbarth, Institut f¨urMedizinische Statistik, Universit¨atsmedizin, Korreferent: Georg-August Universit¨at,G¨ottingen Prof. Dr. Burkhard Morgenstern, Weitere Mitglieder Institut f¨urMikrobiologie und Genetik Abtl. Bioinformatik, der Pr¨ufungskommission: Georg-August Universit¨at,G¨ottingen Prof. Dr. Carsten Damm, Institut f¨urInformatik, Georg-August Universit¨at,G¨ottingen Prof. Dr. Florentin W¨org¨otter, Physikalisches Institut Biophysik, Georg-August-Universit¨at,G¨ottingen Prof. Dr. Stephan Waack, Institut f¨urInformatik, Georg-August Universit¨at,G¨ottingen Tag der m¨undlichen Pr¨ufung: der 30. M¨arz2018
    [Show full text]
  • Analysis of RNA Expression of Normal and Cancer Tissues Reveals High Correlation of COP9 Gene Expression with Respiratory Chain Complex Components Christina A
    University of Kentucky UKnowledge Toxicology and Cancer Biology Faculty Toxicology and Cancer Biology Publications 12-1-2016 Analysis of RNA Expression of Normal and Cancer Tissues Reveals High Correlation of COP9 Gene Expression with Respiratory Chain Complex Components Christina A. Wicker University of Kentucky, [email protected] Tadahide Izumi University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits oy u. Follow this and additional works at: https://uknowledge.uky.edu/toxicology_facpub Part of the Cancer Biology Commons, Cell Biology Commons, and the Medical Toxicology Commons Repository Citation Wicker, Christina A. and Izumi, Tadahide, "Analysis of RNA Expression of Normal and Cancer Tissues Reveals High Correlation of COP9 Gene Expression with Respiratory Chain Complex Components" (2016). Toxicology and Cancer Biology Faculty Publications. 56. https://uknowledge.uky.edu/toxicology_facpub/56 This Article is brought to you for free and open access by the Toxicology and Cancer Biology at UKnowledge. It has been accepted for inclusion in Toxicology and Cancer Biology Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. Analysis of RNA Expression of Normal and Cancer Tissues Reveals High Correlation of COP9 Gene Expression with Respiratory Chain Complex Components Notes/Citation Information Published in BMC Genomics, v. 17, 983, p. 1-14. © The Author(s). 2016 This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2010/0129929 A1 Polakewicz Et Al
    US 20100129929A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0129929 A1 Polakewicz et al. (43) Pub. Date: May 27, 2010 (54) TYROSINE PHOSPHORYLATION SITES (86). PCT No.: PCT/US2007/O16927 (76) Inventors: Roberto Polakewicz, Lexington, S371 (c)(1), MA (US); Charles Farnsworth, (2), (4) Date: Feb. 13, 2010 Concord, MA (US); Ailan Guo, Related U.S. Application Data Burlington, MA (US); Klarisa Rikova, Reading, MA (US); (60) Provisional application No. 60/833,826, filed on Jul. Albrecht Moritz, Salem, MA (US); 27, 2006. Kimberly Lee, Seattle, WA (US); O O Erik Spek, Cambridge, MA (US) Publication Classification (51) Int. Cl. Correspondence Address: GOIN 33/53 (2006.01) Nancy Chiu Wilker, Ph.D. C07K 6/8 (2006.01) Chief Intellectual Property Counsel (52) U.S. Cl. ...................................... 436/501; 530/387.9 CELL SIGNALING TECHNOLOGY, INC., 3 Trask Lane (57) ABSTRACT Danvers, MA 01923 (US) The invention discloses 349 novel phosphorylation sites iden tified in carcinoma, peptides (including AQUA peptides) (21) Appl. No.: 12/309,727 comprising a phosphorylation site of the invention, antibod ies specifically bind to a novel phosphorylation site of the (22) PCT Filed: Jul. 27, 2007 invention, and diagnostic and therapeutic uses of the above. Patent Application Publication May 27, 2010 Sheet 1 of 22 US 2010/0129929 A1 FIGURE 1 Crude protein (e.g., cell extractor cellular organelle) or in vitrokinase reaction or purified phosphoprotein obtain protein fraction (e.g., lysis, organic extraction, detergent
    [Show full text]
  • Rabbit Anti-NR0B1 Antibody-SL10434R
    SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-NR0B1 antibody SL10434R Product Name: NR0B1 Chinese Name: 肾上腺发育不全相关蛋白抗体 NR0B1 / Dax1; AHC; AHCH; AHX; DAX 1; DAX-1; DAX1; Dosage sensitive sex reversal; DSS; DSS AHC critical region on the X chromosome protein 1; DSS-AHC critical region on the X chromosome protein 1; GTD; HHG; Nr0b1; NR0B1_HUMAN; Alias: NROB1; Nuclear hormone receptor; Nuclear receptor 0B1; Nuclear receptor DAX 1; Nuclear receptor DAX-1; Nuclear receptor DAX1; Nuclear receptor subfamily 0 group B member 1; SRXY2. Organism Species: Rabbit Clonality: Polyclonal React Species: Human,Mouse,Rat,Chicken,Pig,Cow,Horse,Rabbit,Sheep, WB=1:500-2000ELISA=1:500-1000IHC-P=1:400-800IHC-F=1:400-800ICC=1:100- 500IF=1:100-500（Paraffin sections need antigen repair） Applications: not yet tested in other applications. optimal dilutions/concentrations should be determined by the end user. Molecular weight: 52kDa Cellular localization: The nucleuscytoplasmic Form: Lyophilizedwww.sunlongbiotech.com or Liquid Concentration: 1mg/ml immunogen: KLH conjugated synthetic peptide derived from human NR0B1:331-430/470 Lsotype: IgG Purification: affinity purified by Protein A Storage Buffer: 0.01M TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Store at -20 °C for one year. Avoid repeated freeze/thaw cycles. The lyophilized antibody is stable at room temperature for at least one month and for greater than a year Storage: when kept at -20°C. When reconstituted in sterile pH 7.4 0.01M PBS or diluent of antibody the antibody is stable for at least two weeks at 2-4 °C.
    [Show full text]